ATLANTA - Cardinal Sean P. O’Malley, the Roman Catholic archbishop of Boston, said Wednesday that he is worried and saddened that the controversy over the Vatican’s rebuke of a US nuns’ group may have fostered a perception the church is inhospitable to women.

O’Malley spoke for the first time about the situation in an interview at a gathering of bishops, as supporters of beleaguered nuns protested outside. Earlier this week, Vatican officials met with leaders of the nuns’ group, but they did not resolve their differences.

“It’s a great concern,’’ he said. “The last thing the church needs is more controversies. As we try to evangelize people, we are trying to get them to focus on the centrality of Christ and trying to promote family life and service to the poor, and I see these things as great distractions sometimes.’’

The vital leadership that nuns and lay women have undertaken in Catholic institutions and parish life shows the esteem in which the church holds them and the “great debt of gratitude’’ all Catholics owe them, O’Malley said.

O’Malley declined to assign blame for what he described as misrepresentation of the church’s attitude toward women, but a spokesman later clarified that O’Malley believes the church hierarchy could do a better job communicating complex subjects and that the media have unfairly characterized the issues and linked matters that are unrelated to one another.

The twice-a-year gathering of the US Conference of Catholic Bishops, held at a large downtown hotel here, did not formally address the Vatican’s recent censure of the Leadership Conference of Women Religious, a professional organization that represents the leaders of 80 percent of the country’s 56,000 sisters.

In April, the Vatican cited the group for seeming to embrace “radical feminism,’’ raising questions about church doctrine on matters such as women’s ordination and failing to actively promote church teaching against abortion and gay marriage. The Vatican appointed the archbishop of Seattle to oversee the Leadership Conference’s activities.

O’Malley said he was not concerned that the sisters had spent too much time on social justice work at the expense of other efforts, but said he agrees with the Vatican’s Congregation for the Doctrine of the Faith that there is little room for discussion or debate on the church’s fundamental beliefs.

“To simply contradict them or dismiss them, and to embrace the values of the secular culture over what the church has taught for 2,000 years, is not acceptable,’’ he said.

Outside the hotel, about three dozen nuns and lay people affiliated with the Nun Justice Project, a coalition of left-leaning Catholic groups that has held more than 50 vigils for the nuns nationwide in the last two months, presented a petition with more than 57,000 signatures supporting the nuns. They held signs that said, “Jesus was a radical feminist,’’ and “You can’t undo Vatican II.’’

Carol Cornelius of Atlanta, 77, said she attended a local church service recently and witnessed a priest offer a powerful homily supporting the sisters.

Turning to a friend, she said, “I said, ‘I feel like clapping.’ And at that point, everyone in the church did.’’

Sister Mary Ann Walsh, director of media relations for the US Conference of Catholic Bishops, accepted the petition on behalf of the bishops. Walsh, a member of the Sisters of Mercy of the Americas, said the prelates hoped the issue could be resolved “prayerfully and collaboratively.’’

“The bishops are clearly aware of all that the sisters have done in this country to build the school system and hospital system and today building new systems to address new problems,’’ she said.

Sister Patty Caraher, 78, a Dominican sister of Sinsinawa who helped found a school for refugee children in Atlanta, was another protester. She said each women’s religious congregation spends hours praying over and deliberating what Jesus wants it to do for the church and for the needy.

“For us to have someone tell us we are going to be monitored, in this day and age, as women, it’s offensive,’’ she said.

O’Malley said the nun dispute is about the specific activities of the Leadership Conference, not about US nuns at large.

“I feel terrible that these difficulties between the [Leadership Conference] and the Holy See have come across as being any kind of indictment of women religious in this country,’’ he said. “That’s not true. I think we have nothing but affection for them.’’

And, he said, it is unfair to link any of the recent clashes between the church hierarchy and individual women or women’s groups: The Vatican’s rebuke of the Leadership Conference; the condemnation of a sexual ethics book written by Sister Margaret Farley, a retired Yale Divinity School theologian; or the US bishops’ decision to investigate the Girl Scouts of America.

“Obviously, when people are trying to portray the church as being antiwomen - it’s very disturbing and hurtful,’’ he said.

O’Malley noted that another Vatican investigation of the quality of life in women’s religious communities, which started out on a tense note several years ago and wrapped up at the end of last year, appears to have ended amicably, essentially affirming the lives of the women and their contributions to the church and society.